The aim of the present study was to identify genes whose expression and/or organisation are altered in the diseased breast, as compared to the normal breast. Alteration of one or more genes examined has been found to occur in over 60% of breast tumour samples. Changes to three cellular proto-oncogenes are frequent, and amplification of two of these genes correlates with poor short-term prognosis. Deletion of RB-1, a tumour suppressor gene, has been detected and although these deletions do not correlate with poor prognosis, they occur more commonly in advanced tumours. A loss of sequences encoding the progesterone receptors has also been found to be frequent.